Vector Xpression™ 3 - Thermo Fisher Scientific
Contents
1. Before beginning this tutorial complete the following actions if you have not yet performed them 1 Install Vector Xpression 3 For more information about installing Vector Xpression 3 see the Vector Xpression 3 Installation Guide that can be accessed from the InforMax Web site http www informaxinc com vnti vntisuite Installation VXpression lt date gt pdf In Windows click Start gt Settings gt Control Panel Click Display In the Display Properties dialog box make sure that Colors is set to a minimum of High Color 16 bit Lower settings will cause scatter plots shown in this tutorial to display black If you have completed Steps 1 and 2 listed above proceed with this tutorial Speed Tutorial Part Importing Two Channel Expression Raw Data Introduction Purpose Reference Experiment Overview Expression Data Sets This Speed tutorial teaches you to import two channel expression data producing a raw data object in the Vector Xpression database It is part of a series of three tutorials to teach you how to use Vector Xpression l Importing Two Channel Expression Raw Data II Adding Annotations IIl Creating a Script for Automating Data Normalization Other tutorials are available from InforMax to teach you other methods of using Vector Xpression Refer to the InforMax website for more information http www informaxinc com content cfm pageid 25 The Speed tutorial is based on the microarray2. selected you can see all the raw data objects you have just imported with their chip name Speed_1 assigned to each ector Xpression Database C NTI Database Speed Tutorial_1 mdb l O x Table Edit Yiew Database Tools Help E Raw Data SS lt lt gt 929 Gs fa ae K Be ayy All database Raw Data Description Chip Name DataType alll Speed tutorial Speed 1 cDNA Speed 1 cDNA Speed 1 cDNA Speed 1 cDNA Speed 1 cDNA Speed 1 cDNA Selected 0 Raw Data 6 Raw Data Figure 22 The Xpression Database Explorer displays imported files You have successfully built the chip design associated it with six files of raw data and saved the chip to the Vector Xpression database Now you will continue to Part Il Adding Annotations optional and or Part Ill Creating a Script for Automating Data Normalization 16
3. the text boxes as shown in Figure 15 if they are not entered by default b Click Next gt to continue 7 Insure that the Data File button is still active in the Import window 12 Speed Tutorial Part Importing Two Channel Expression Raw Data 8 The Coordinates dialog box opens Figure 16 Coordinates Enter position of coordinates lt Back Cancel Figure 16 Designate column coordinates in the Coordinates dialog box a Click in the text box in the Col column adjacent to BlockY coordinate and in the drop down list that appears select 2 b Repeat the process selecting 3 4 and 5 for the BlockX Y and X rows respectively as illustrated in Figure 21 c Click Next to continue 9 In the Gene Name column dialog box Figure 17 a Enter 8 in the Column text box Enter position of Gene Name column Column E lt Back Finish Cancel Help Figure 17 Gene Name dialog box b Click Finish In the dialog box that opens enter the Scheme Name to continue At this point in the tutorial you will import all of the text files necessary to complete the series of three Speed tutorials 1 You are returned to the Assign Schemes to Selected Files dialog box Figure 18 a Click in the uppermost cell in the Scheme column then SHIFT CLICK on the lower most cell This selects all of the rows and a drop down text box displays in the lowest box b Inthe t
4. txt File name sample bo bat sample ce tet sample ca tet Files of type Text files Cancel Delimiter Tab Whitespace Semicolon C Other Figure 3 Select Expression Data File s to Import Dialog Box a Inthe Look in list navigate to the directory where you saved the source data files Do not click Open yet In the Files of type list select Text files CONTROL CLICK the Sample c1 c2 and c3 txt files and the Sample t1 t2 and t3 txt files in the area below the Look in list d Inthe Delimiter area accept Tab e Click Open 2 This opens the Assign Schemes dialog box Figure 4 Assign Schemes to Selected Files a i i i ioj x File Path E ector Documentation ector Xpression da EWector Documentationector Xpression da een new a E Wector Documentation ector Apressianida Affymetrix Raw Data Speed 1 E Wector Documentation ector spressionida Raw Data Speed 1 ee E Wwector Documentation ector Xpressionida E Wwector Documentation ector Apression da bP _ Add File Remove File Import Cancel Speed Tutorial Part Importing Two Channel Expression Raw Data Figure 4 Assign Schemes to Selected Files dialog box a Click in the upper most empty text box in the Scheme column b On the drop down list that appears select lt Create new Scheme gt Figure 5 3 Inthe Import Data File Type dialog box that opens select the Raw Data radio button and click O
5. 1 2 16 8655 22 0 41 5819 72 0 29 1500 44 719 39 37 1 1 2 17 3715 55 1 09 2596 45 0 11 1079 01 739 40 38 1 1 2 18 6860 31 0 51 4211 38 0 27 1574 02 749 AA 320 4 4 be he oi 4a 4547219 naa AERA a noT ART EN MR 4 gt Figure 13 Chip Design Window Still in the Coordinates dialog box now you will change the terminology for your selections Figure 14 11 Speed Tutorial Part Importing Two Channel Expression Raw Data Choose Gene ID or Spot Coordinates columnis C Gene IDs in column i Spot Coordinates zi Use the Delete button to delete a entire entry lt Back Cancel Help Figure 14 Coordinates Dialog Box Click in the cell labeled grid_r Click the down arrow and select BlockY from the drop down list f Repeat the process for the grid_c spot_r and spot_c entries replacing them with BlockX Y and X respectively d Click Next gt to continue At this point the Chip Design File button in the Import window becomes acti and the contents of the chip design file now display in the spreadsheet 5 The Header and Data dialog box opens Figure 15 Enter position of header and data Data position Header at row Data begins at row 2 H Data ends at row kEnd of file gt aj Use advanced settings Advanced lt Back Cancel Help Figure 15 Header and Data dialog box a Enter the appropriate rows in
6. 6 0 39 1577 31 0 18 1048 49 954 6 4 1 1 1 5 1321 75 0 26 1525 48 0 17 876 52 857 7 5 1 1 1 6 1055 64 0 36 1520 95 015 890 94 874 8 6 1 1 1 7 18564 73 0 49 14831 04 0 6 1419 14 786 9 7 1 1 4587 5 0 45 1655 51 856 10 8 1 1 6854 41 0 35 1944 14 775 11 9 1 1 Choose Gene ID or Spot Coordinates columnis 3021 22 0 28 1275 22 880 12 10 1 1 a 7019 0 73 1172 58 731 13 11 1 1 11409 09 018 2580 54 792 14 12 1 1 5265 16 0 11 1665 89 758 1S 13 1 1 Gene IDs in column fi 4 1979 09 0 25 820 03 743 16 14 1 1 icy Spot Coordinates 3042 5 0 34 1161 52 725 17 15 1 1 1784 67 0 42 798 73 747 18 16 1 1 Coordinate 3295 75 0 2 1360 4 682 19 17 1 1 grid_r 2 10544 11 0 28 1269 02 674 20 18 1 1 grid_c 3 247517 0 4 940 01 664 21 Data 19 1 1 4019 17 0 38 1008 36 596 22 20 1 1 3172 85 02 909 04 632 23 21 1 1 14659 25 1 03 1366 29 1232 24 22 1 1 6470 76 0 27 1815 99 1331 25 23 1 1 7474 59 0 19 2043 62 1053 26 24 1 1 10048 92 0 5 1886 95 1027 27 25 1 1 2093 24 0 37 943 35 924 28 26 1 1 2136 64 0 28 977 01 938 29 27 1 1 3275 08 0 51 1046 66 811 30 28 1 1 2 8 6245 1 0 38 4784 8 0 37 1149 96 808 31 29 1 1 2 9 6308 22 0 41 5380 22 0 23 1246 6 840 32 30 1 1 2 10 15598 62 0 57 8869 15 0 37 2241 74 805 33 31 1 1 2 11 2355 62 0 35 1987 56 0 25 841 69 700 34 32 1 1 2 12 10128 75 0 57 5758 38 0 26 1270 35 767 35 33 1 1 2 13 206937 0 85 14244 63 0 84 962 16 668 36 34 1 1 2 14 16998 72 3 23 13560 47 2 43 728 16 679 37 35 1 1 2 15 13325 93 1 57 10424 23 1 29 808 64 629 38 36 1
7. K Figure 6 xi What kind of data does this file contain Pre processed Data Cancel A ee Ww qs oo ra Figure 5 Selecting the data type to be imported The Import window containing a spread sheet view of the selected raw data source file opens Figure 6 It is superimposed by the Header and Data dialog box Dala File Sawe file DASHTI Epron Date nonmponsd Da tet ali Zz Roan i 1 Header Index ORF Gl G1 Dkg RI Rika 1 i THROOS YERZ1BC ALLO 4 YALOSSW 6762 2107 6343 1070 YALOSAC s _ YALOSSW 7 TAL S a A WALOSEW VOL NOH TALOGSC Tz 11 TALDEPA Enter position of header amd data El 1 VALIGE Diste portion 1a 13 WAPOA WAPOA j eae T 15 1 YAROUZW a Header 16 15 YARONPA Data bagni at roer It E 17 16 TALOO IC E Jd 18 17 YALOOT Daamin iEnd tt ia Data 18 ALOE 20 E TALITA al 20 WALOOSC 22 i YALUOFE 27 YALOOEW YALU WALOIOC ALO Tw TALUS O Use advanced a Aa IFI Aan Tian Zr FALOL Sa 1923 1376 965 0 23 eu TALO LAG PEF dtl Jezi 1406 0 30 29 FALOLSC a217 2050 22193 Lil i a1 Jy TALO IUA Eat Pi fa Sha 12us 0 TE 51 TALIITA ara 1753 tere 1 Gn fi KE gz TALO PE 3240 zrah 1590 1299 0 gal 537 TALDEA 5597 157 AET loa 3 EC TALODOL Sear 261 afi 1355 0 KT J9 TALUZIG bie 1EY ey REE 0 Aor SR RGM ADS Ee gr dowi Em ROWS SOR SOA om Figure 6 Import Dialog Box Data
8. Vector Xpression 3 Speed Tutorial Part I Importing Two Channel Raw Data 8 InforMax Invitrogen life science software Speed Tutorial Part Importing Two Channel Expression Raw Data Table of Contents Important Please Read 2 00 ecccccceccecceeeceeeeeeceeceeeeseceeceeeseeceeesnececseeceeseesgeteeeeeecaeeaeeteeseeseeeegeetes 1 Creating a New Vector Xpression Database ccccecccceccceeeceececeeeeauceceeeseueesueecsueesueeseeesaeeesaees 3 Opening the Raw Data Source File ccc ccccceccceececceceececeeeeaeeeseeeeseceseeessuceseesaneeseeessueeaeeesaees 4 Viewing and Defining Raw Data in the Source File cecccccccecccceeeceeeeaeeeceeeeeeeseeesseeeseeesaneees 7 Building the Chip De SIQN ccccecccceccceececeeeceeeeaeeeceeeeseeeeeeeeseeeseeeeeueeseeessueeseeeeseeesneesneeseeesaees 10 Finalizing Import Important Please Read This tutorial assumes that you are familiar with the standard Windows user interface and basic Windows techniques such as maximizing windows selecting objects Zooming in and out on objects switching between panes in a viewer window etc For more information about basic Windows operations see Chapter 3 of the Vector Xpression 3 User s Manual It also assumes that you are somewhat familiar with gene expression techniques and data For more information see the Gene Expression Overview section in Chapter 4 of the Vector Xpression 3 User s Manual
9. ced west 29 1 1 2 g 32 30 1 1 2 10 33 31 1 1 2 11 a a 1 z i Bac Cancel Help 35 33 1 1 2 13 Mstart CO GUM amp BAES Dy Qs wi Od way Cy YF Si Sid Gs eE SACS 590UB90M im Figure 7 Open source file displaying experimental data Speed Tutorial Part Importing Two Channel Expression Raw Data 2 In the Header and Data dialog box Figure 8 verify or enter the following a Enter the appropriate rows in the Header and Data text boxes as shown in Figure 9 if they are not entered by default Selecting End of file for Data end instead of specifying the row containing the end of the data allows flexibility when this scheme is used on future files Header and Data Enter position of header and data Data position Header at row Ir Data begins at row 2 H Data ends at row kEnd of file gt a Use advanced settings 9 Advanced Figure 8 Header and Data dialog box b Click Next to continue 3 The Select Number of Channels dialog box opens Figure 9 Channels Enter number of channels How many channels does this experiment contain One Channel Single color experiment Figure 9 Channels Dialog Box a Select the Two Channels Two color experiment radio button b Click Next to continue 4 The Data dialog box opens Figure 10 Speed Tutorial Part Importing Two Channel Expression Raw Data Select what numerical channel information you will i
10. data produced and analyzed by Callow MJ Dudoit S Gong EL Speed TP and Rubin EM 2000 Microarray expression profiling identifies genes with altered expression in HDL deficient mice Genome Res 10 2022 2029 This experiment surveys the effects of a knockout of the apoAl gene in mice on the expression of other genes in the liver Livers from mice homozygous for the apoAl knock out on a C5 BI 6 background as well as control C57BI 6 mice were obtained total RNA extracted and the individual samples from each liver reverse transcribed using Cy5 dUTP The reference RNA was a pool of total RNA obtained from the livers of eight C57BI 6 mice reverse transcribed with Cy3 dUTP To download this paper in pdf format click the following link http www genome org cgi content full 10 12 2022 Because this tutorial uses the same data analyzed in the publication you can download a file containing all of the original expression data from the author s Web page http stat www berkeley edu users terry zarray Html apodata html For the purposes of this tutorial however you will use six separate raw data files created from the original data text file You can retrieve them from this site http stat www berkeley edu users terry zarray Software smacode html Click on the tar file link by the Data Files section Click Open in the File Download dialog box unzip the files and save them on your hard drive Open each file in Notepad and save it as a t
11. ext box drop down menu select Raw Data Speed_1 import scheme 13 Speed Tutorial Part Importing Two Channel Expression Raw Data 4ssign Schemes to Selected Files 15 x gt A Documents gt A Documents I C Documents C Documents gt A Documents Documents and Settings and Settings and Settings and Settings and Settings and Settings erandle De erandleDesk erandle De erandle De erandle De werandle De sktop WE Raw Data Speed_1 sktopit sktop s sktop s sktop s C Documents and Se lt Create new Schemer Affymetrix Raw Data Codelink Raw Data Genepix Add File 2 aaa Fie Canad Figure 18 Assign Schemes dialog box selecting the import scheme c Click the Import button The Finalize Import dialog box opens The Assign Schemes to Selected Files dialog box returns to view The Chip Design cell in this dialog box now indicates that the chip design information is derived from the source file opened in the Import dialog box It is assigned to all six files you are importing Now you will process the data in the file for mapping into the Vector Xpression database Finalizing Import Overview The Finalize Import dialog box in which you will finalize import displays a summary of the file features for the database and allows you to change them if necessary It also allows you to name the column headers used in the spreadsheets of the Vector Xpression
12. ext file indicated by the txt extension to each file name Speed Tutorial Part Importing Two Channel Expression Raw Data Additional Notes About the Data Sets IMPORTANT The data sets used in this tutorial are a subset of the original data and are distributed as part of the Speed group s R program SMA Statistical Microarray Analysis package This subset of the original data was chosen for two reasons 1 the data from the author s website is only available as an R data frame which needs extensive manipulation for converting into a format suitable for Vector Xpression 2 the full apoA1 data frame is a Summarized version of the original data only containing the background corrected fluorescence intensity values The relationships between the files used in this tutorial and the columns in the file containing the full apoAl data set available from the author s website are listed in Table 1 Data File Sample Cy5 channel Reference Cy3 Channel sample c1 txt c1G sample c2 txt Table I Components of text files comprising the Speed data sets You may want to use this tutorial in conjunction with the Vector Xpression 3 User s Manual for clarification of all functionality Creating a New Vector Xpression Database Overview Vector Xpression saves information such as raw data chip designs and layouts as database objects which are then stored in a relational database The Vector Xpression Database Explorer o
13. from Source File You have successfully opened the raw data source file Now you will view and define the raw data source file for import Speed Tutorial Part Importing Two Channel Expression Raw Data Viewing and Defining Raw Data in the Source File Overview In configuring an expression data file for import the main Import dialog box opens displaying the source file After your source file is loaded browse the source data to familiarize yourself with it This source file remains open for your referral as you step through each window using the Import Wizard The source file used to build the import scheme presents a complete dataset of one microarray experiment Data presented in the source file are absolute signals real measurements read from a chip containing a specific number of genes One channel data represents values read from one experiment Two channel data represents one experiment in which RNA from a sample was labeled during reverse transcription with the red fluorescent dye Cy5 and was mixed with a sample labeled in parallel with the green fluorescent dye Cy3 This tutorial uses data from two channel experiments The first dialog box of the Import Wizard the Header and Data dialog box is superimposed on the Import window To better review the source file click on the blue title bar of the dialog box and drag it out of the way 1 Inthe open source file note the location of the Header row and Data start and end rows Fi
14. gure 7 The Header is the first row in the file and usually contains the column names The data is contained in rows 2 through 6385 Source file E Wector Documentation Vector lt pression datasets S MA from berkeley link Speed tut sample c1 txt caja 2 3 E IE 6 7 8 IE IE Row a 1 Header indexs grid_r grid_c spot_r spot_c Gmean GIOQR Rmean RIQR 2 lo 1 1 1 1 6256 08 1 05 4184 08 0 97 fi 1 1 1 1 2 5389 81 1 15 4148 48 0 93 a3 4 2 1 1 1 3 2653 29 0 44 2452 32 0 35 5 9 A 1 1 4 1071 26 0 39 1577 31 0 18 6 4 1 1 1 5 1321 75 0 26 1525 48 0 17 E 5 1 1 1 6 1055 64 0 36 1520 95 0 15 a 6 1 1 1 7 18564 73 0 49 14831 04 0 6 9 7 1 1 1 8 9974 0 66 4587 5 0 45 10 8 1 1 1 9 10721 71 0 25 6854 41 0 35 11 9 1 1 1 10 3550 72 0 35 3021 22 0 28 12 10 1 1 1 11 9557 5 0 73 7019 0 73 13 11 1 1 1 12 17659 75 0 21 11409 09 0 18 14 12 1 1 1 13 9605 47 0 3 5265 16 0 11 15 13 1 1 1 14 1702 09 0 29 1979 09 0 25 16 14 1 1 1 15 Header and Data AT 15 1 1 1 16 17 a S Data is 1 u Enter position of header and data 19 17 1 1 1 18 a 20 18 1 1 1 19 S S 21 19 1 1 1 20 2 F 20 1 1 1 21 ae Data position 23 21 1 1 2 1 24 22 1 1 2 2 Header at row 25 23 1 1 2 3 J Data begins at row 2 a 26 24 1 1 2 4 gt 3 zi 27 25 1 1 2 5 Data ends at row kEnd of file gt a 28 26 1 1 2 6 L Ls 27 1 1 2 7 30 28 1 1 2 8 Use advanced settings Advan
15. me sample gnames TXT Files of type Text files Cancel Delimiter Tab Whitespace Semicolon C Other Figure 12 Select the Chip Design File for your expression data 10 Speed Tutorial Part Importing Two Channel Expression Raw Data Select the file sample gnames TXT whose name now displays in the File name field Select Text files from the drop down list in the Files of type text box From the Delimiter radio buttons select Tab Click the Open button 3 Back in the Chip Design Information Source dialog box click Next gt to continue a9 5 4 The Coordinates dialog box is now superimposed on the source file a Select the Spot Coordinates radio button b Drag the column header named grid_r to the top text box in the Coordinate column c Drag the column headers in the spreadsheet named grid_c spot_r and spot_c to consecutive rows as illustrated in the dialog box in Figure 13 lai x Data File Chip Design File Source file 1 D PD WXX pression 3 Miscellaneous SMA SMA_Data sample cl TXT Col 1 2 3 4 5 6 7 8 g ja mE Row Signal Channel 2 Signal Channel 1 Background Chai 1 Header indexs grid_r grid_c spot_r spote ss Gmean GIQR Rmean RIQR bgGmean bgGn 2 0 1 1 1 1 6256 08 1 05 4184 08 0 97 1502 91 1246 3 1 1 1 1 2 5389 51 115 4148 48 0 93 1390 36 1198 4 2 1 1 1 3 2653 29 0 44 2452 32 0 35 1257 46 1088 5 3 1 1 1 4 1071 2
16. mport If importing additional data click on the black arrow and give the heading name Background llenn Background corrected signal Signal Background ratio Back Cancel Help Figure 10 Data Enter the data you will import Dialog Box c Select the Signal and Background check boxes Signal and Background are the names for the relevant data columns to be used in Vector Xpression In the source file Figure 7 on page 7 note that columns 6 and 10 contain signal and background data for one channel and columns 8 and 13 contain signal and background data for the other channel d Click Next to continue 5 The Assign Columns to Channel Data dialog box opens e Enter the appropriate column numbers in the text boxes as shown in Figure 11 Verify the entries by reviewing the corresponding data in the source file To enter the information easily click on each appropriate column header in the spreadsheet view and drag it to the respective text box To enter figures manually click twice in each cell activating the text box and type the correct number Assign Columns to Channel Data Assign the correct columns to the data You can do this by typing in the number or drag and drop the header of column Signal 5 Sample gna Background 13 Reference ana i Background 10 Back Mest gt N Cancel Help Speed Tutorial Part Importing Two Channel Expression Raw Data Figure 11 Assign Columns t
17. o Channel Data Dialog Box f Click Next to continue 6 Inthe Additional Spot Data dialog box that opens verify that the checkboxes are unchecked Click Next gt to continue 7 Inthe second Additional Spot Data dialog box that opens verify that the check boxes are unchecked Click Next gt to continue 8 The Chip Design Information Source dialog box opens to begin the next phase of the import process You have successfully viewed and defined the raw data source file Now you will build the chip design and associate it with the raw data Building the Chip Design Overview To continue the import you must build the chip design and associate it with the raw data Chip designs link the spot locations of Raw Data objects to their gene names 1 The Chip Design Information Source dialog box allows you to identify the source file that provides information about the configuration of a given microarray chip If the file were the file you already have open you would select the radio button This File In this case however select Another file and click the Browse button t 2 Inthe Select file s to Import dialog box Figure 12 navigate to the folder containing the chip design file to be loaded Select file s to import x Look in E SMA_Data e M EJ sample c1 TXT E sample t2 TXT sample c2 TXT sample t3 TXT eee sample ca TAT z sample exp TAT sample gnames TAT sample tl TXT File na
18. oligdata AnalysesT able C ExpressionDB C ProData BLASTSearch CI GMData C Tables BLASTSearchAppDB C MedLineStyle CI vecContData Citation J MolData CntData I MotData File name Speed Tutorial_1 Save as type Microsoft Access Files mdb Cancel Me Figure 2 Select a Location of a New Database Dialog Box 3 Inthe Select a Location of New Database dialog box Figure 2 name the new database file Speed_Tutorial_1 navigate to a convenient drive and folder for saving the new file and click Save This returns you to the Vector Xpression Database viewer window displaying the new blank database Now you will load the first raw data set into the empty database Opening the Raw Data Source File Overview Using a raw data text file you will create an import scheme and load the raw data into Vector Xpression using the Import Tool Vector Xpression s dual purpose tool called Import creates the necessary import scheme for an expression data file and then uses that scheme to import the expression data file into Vector Xpression This produces a Raw Data object in the Vector Xpression database Speed Tutorial Part Importing Two Channel Expression Raw Data 1 In the Vector Xpression Database Explorer select Tools gt Import Expression Data The Select File s to Import dialog box displays Figure 3 Cee Select file s to import sample c1 txt sample cz txt sample c txt sample txt sample be
19. rganizes these expression objects for easy retrieval and management Additionally it supports intuitive browsing of databases drag and drop operations and other functions typical of window based database management From the Explorer window you can perform the following operations e Open raw data objects Expression Runs Runs Projects and expression experiments Sort edit and delete items Search the database Organize your data into convenient groups subsets Exchange database objects among databases and subsets Import and export data You will use the Database Explorer to import the data Speed Tutorial Part Importing Two Channel Expression Raw Data 1 From the Windows Start button select Start gt Programs gt InforMax 2003 gt Xpression Explorer to open the Vector Xpression Database Explorer Figure 1 10 x Table Edit Yiew Database Tools Help E Raw Data J eS om sy All database Raw Data tal A ale X Et EB ai 2 Name Description ChipName Datatype l E DeRisi_9 DeRisi cDNA E DeRisi_13 DeRisi cDNA MB DeRisi_15 DeRisi cDNA B DeRisi_16_5 DeRisi cDNA MB DeRisi_18_5 DeRisi cDNA WB DeRisi_21 DeRisi cDNA MlpeRisi 11 5 DeRisi cDNA zl Selected 0 Raw Data 7RawData Figure I Opening Vector Xpression Database 2 From the Vector Xpression Database menu bar select Database gt New Empty Database Save in VNT Database e ce EJ AM JenzData 1
20. viewers This dialog box has three tabs and it opens to the tab appropriate to the data type you are importing If necessary left click and drag the window borders or the dividers between the column headings to readjust the window size or column widths to see the column contents 14 Speed Tutorial Part Importing Two Channel Expression Raw Data In the Finalize Import dialog box cells there are three methods you can use to enter or edit information for the specified data IMPORTANT Click in a blank cell or a cell with text you want to edit One or more of three options may appear Click on the down arrow x to reveal a drop down list Click on the Browse button Eh to open a navigation dialog box Click on the Text icon LT to activate the text box where you can enter or edit text 2 Inthe Finalize Import dialog box in the blank cell in the Chip column select the browse button L h Figure 19 Finalize Import x Two Channel Raw Data One Channel Raw Data Expression Runs Channel Name Target Name File Hame Spots Genes Sample Reference Sample Reference sample ct l B E i Channel 1 Channel 2 Channel 1 Channel 2 sample c2 Channel 1 Channel 2 Channel 1 Channel 2 sample c3 Channel 1 Channel 2 Channel 1 Channel 2 sample t1 Channel 1 Channel 2 Channel 1 Channel 2 sample t2 Channel 1 Channel 2 Channel 1 Channel 2 sample t3 Channel 1 Channel 2 Channel 1 Channel 2 Figure 19 Finali
21. ze Import dialog box assigning the chip 3 Inthe Create New Chip dialog box name the new chip object Speed_7 and click the Create button Figure 20 Create New Chip f x Select Subset Physical Chips New subset Mame Speed 1 Description Cancel Figure 20 Create New Chip Dialog Box Back in the Finalize Import dialog box you can see in the Chip column the name of the new chip you ve just created 15 Speed Tutorial Part Importing Two Channel Expression Raw Data 4 Use SHIFT CLICK to select all the rows in the Chip column and choose Speed_1 from the dropdown menu to assign this chip to all six files Assigning the chip as you have just done is the only essential step required for this part of the import process You can however edit other fields in the dialog box using the edit techniques previously described 5 6 Click Save to DB In the Choose Subset dialog box only the top level Raw Data table the root directory is listed Figure 21 Name a new subset in the Name text box Speed Tutorial and click OK This is the subset where the data is to be stored Raw Data Subset Mame cel Figure 21 Select Subset Dialog Box When prompted select the Yes button to close the Import dialog box This verifies that the data you just imported resides in the Vector Xpression Database You are returned to the Vector Xpression Database Explorer Figure 22 With the Raw Data table
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